Bacteria commonly express enzymes in metabolic pathways using polycistronic mRNAs that encode the sequences of multiple genes. Translation of these genes is governed by a phenomenon known as translational coupling, which ties the expression levels of downstream genes within the mRNA to those located upstream. The atp operon in E. coli, for instance, provides a well-known example of translational coupling. In this operon, translation of the downstream gene (atpA) is normally blocked by a hairpin secondary structure at the end of the upstream gene (atpH). The inhibitory mRNA hairpin only opens to allow translation of atpA when the upstream atpH is being translated.
Despite their widespread use in nature, it has been difficult to rationally engineer the translational coupling between genes on the same polycistronic transcript and efforts to engineer synthetic translational couplers remain in their infancy. The translational efficiency of the downstream gene is strongly dependent on the secondary structure of the ribosomal binding site (RBS) and start codon, yet these features change with each modification to nearby sequences at the end of the upstream gene. Moreover, translational coupling is tied to the procession of the ribosome along the mRNA, a dynamic ribonucleoprotein interaction that is far harder to model than RNA secondary structures alone. Accordingly, there remains a need in the art for a synthetic RNA-based mechanism for detecting translation and modulating expression of a downstream gene without the need for any changes to the output protein sequence.